Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) has simplified and enhanced the quantification of gene expression. However, since no agreed standardizations are available, care must be exercised when designing experiments, including the choice of appropriate amplification primers, detection chemistry and the normalization procedure, in order to obtain meaningful results. Coupling quantitative polymerase chain reaction (qPCR) to cell purification from tumor tissue has made it possible to decrease the variability in expression from in vivo heterogeneous cell populations. Sensitive and specific qRT-PCR has advanced the diagnosis, prognosis and prediction response of colorectal cancer to therapy.